diff --git a/.github/workflows/__with-checkout-path.yml b/.github/workflows/__with-checkout-path.yml
new file mode 100644
index 0000000000..a3b91703ea
--- /dev/null
+++ b/.github/workflows/__with-checkout-path.yml
@@ -0,0 +1,84 @@
+# Warning: This file is generated automatically, and should not be modified.
+# Instead, please modify the template in the pr-checks directory and run:
+#     pip install ruamel.yaml && python3 sync.py
+# to regenerate this file.
+
+name: PR Check - Use a custom `checkout_path`
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  GO111MODULE: auto
+on:
+  push:
+    branches:
+    - main
+    - v1
+  pull_request:
+    types:
+    - opened
+    - synchronize
+    - reopened
+    - ready_for_review
+  workflow_dispatch: {}
+jobs:
+  with-checkout-path:
+    strategy:
+      matrix:
+        version:
+        - stable-20210308
+        - stable-20210319
+        - stable-20210809
+        - cached
+        - latest
+        - nightly-latest
+        os: [ubuntu-latest, macos-latest, windows-2019]
+    name: Use a custom `checkout_path`
+    runs-on: ${{ matrix.os }}
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v2
+    - name: Prepare test
+      id: prepare-test
+      uses: ./.github/prepare-test
+      with:
+        version: ${{ matrix.version }}
+    - uses: actions/checkout@v2
+      with:
+        ref: 474bbf07f9247ffe1856c6a0f94aeeb10e7afee6
+        path: x/y/z/some-path
+    - uses: ./../action/init
+      with:
+        tools: ${{ steps.prepare-test.outputs.tools-url }}
+      # it's enough to test one compiled language and one interpreted language
+        languages: java,javascript
+        source-path: x/y/z/some-path/tests/multi-language-repo
+        debug: true
+
+    - name: Build code
+      shell: bash
+      run: x/y/z/some-path/tests/multi-language-repo/build.sh
+    - uses: ./../action/analyze
+      with:
+        checkout_path: x/y/z/some-path/tests/multi-language-repo
+        ref: v1.1.0
+        sha: 474bbf07f9247ffe1856c6a0f94aeeb10e7afee6
+        upload: false
+      env:
+        TEST_MODE: true
+    - uses: ./../action/upload-sarif
+      with:
+        ref: v1.1.0
+        sha: 474bbf07f9247ffe1856c6a0f94aeeb10e7afee6
+        checkout_path: x/y/z/some-path/tests/multi-language-repo
+      env:
+        TEST_MODE: true
+
+    - name: Verify SARIF
+      run: |
+        cat ../results/java.sarif
+        echo '------------------------------------'
+        echo '------------------------------------'
+        echo '------------------------------------'
+        echo '------------------------------------'
+        cat ../results/javascript.sarif
+    env:
+      INTERNAL_CODEQL_ACTION_DEBUG_LOC: true
diff --git a/lib/actions-util.js b/lib/actions-util.js
index 2102ab64a7..3c1f2ca88b 100644
--- a/lib/actions-util.js
+++ b/lib/actions-util.js
@@ -73,7 +73,7 @@ exports.getToolCacheDirectory = getToolCacheDirectory;
 /**
  * Gets the SHA of the commit that is currently checked out.
  */
-const getCommitOid = async function (ref = "HEAD") {
+const getCommitOid = async function (checkoutPath, ref = "HEAD") {
     // Try to use git to get the current commit SHA. If that fails then
     // log but otherwise silently fall back to using the SHA from the environment.
     // The only time these two values will differ is during analysis of a PR when
@@ -93,6 +93,7 @@ const getCommitOid = async function (ref = "HEAD") {
                     process.stderr.write(data);
                 },
             },
+            cwd: checkoutPath,
         }).exec();
         return commitOid.trim();
     }
@@ -112,6 +113,7 @@ const determineMergeBaseCommitOid = async function () {
         return undefined;
     }
     const mergeSha = (0, util_1.getRequiredEnvParam)("GITHUB_SHA");
+    const checkoutPath = getRequiredInput("checkout_path");
     try {
         let commitOid = "";
         let baseOid = "";
@@ -136,6 +138,7 @@ const determineMergeBaseCommitOid = async function () {
                     process.stderr.write(data);
                 },
             },
+            cwd: checkoutPath,
         }).exec();
         // Let's confirm our assumptions: We had a merge commit and the parsed parent data looks correct
         if (commitOid === mergeSha &&
@@ -424,6 +427,9 @@ async function getRef() {
     // or in the form "refs/pull/N/merge" on a pull_request event
     const refInput = (0, exports.getOptionalInput)("ref");
     const shaInput = (0, exports.getOptionalInput)("sha");
+    const checkoutPath = (0, exports.getOptionalInput)("checkout_path") ||
+        (0, exports.getOptionalInput)("source-root") ||
+        (0, util_1.getRequiredEnvParam)("GITHUB_WORKSPACE");
     const hasRefInput = !!refInput;
     const hasShaInput = !!shaInput;
     // If one of 'ref' or 'sha' are provided, both are required
@@ -445,15 +451,14 @@ async function getRef() {
     if (!pull_ref_regex.test(ref)) {
         return ref;
     }
-    const head = await (0, exports.getCommitOid)("HEAD");
+    const head = await (0, exports.getCommitOid)(checkoutPath, "HEAD");
     // in actions/checkout@v2 we can check if git rev-parse HEAD == GITHUB_SHA
     // in actions/checkout@v1 this may not be true as it checks out the repository
     // using GITHUB_REF. There is a subtle race condition where
     // git rev-parse GITHUB_REF != GITHUB_SHA, so we must check
     // git git-parse GITHUB_REF == git rev-parse HEAD instead.
     const hasChangedRef = sha !== head &&
-        (await (0, exports.getCommitOid)(ref.replace(/^refs\/pull\//, "refs/remotes/pull/"))) !==
-            head;
+        (await (0, exports.getCommitOid)(checkoutPath, ref.replace(/^refs\/pull\//, "refs/remotes/pull/"))) !== head;
     if (hasChangedRef) {
         const newRef = ref.replace(pull_ref_regex, "refs/pull/$1/head");
         core.debug(`No longer on merge commit, rewriting ref from ${ref} to ${newRef}.`);
diff --git a/lib/actions-util.js.map b/lib/actions-util.js.map
index e74d66f57c..81fff98d94 100644
--- a/lib/actions-util.js.map
+++ b/lib/actions-util.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/lib/upload-lib.js b/lib/upload-lib.js
index 3290c42063..be6c2aab36 100644
--- a/lib/upload-lib.js
+++ b/lib/upload-lib.js
@@ -134,7 +134,7 @@ exports.findSarifFilesInDir = findSarifFilesInDir;
 // depending on what the path happens to refer to.
 // Returns true iff the upload occurred and succeeded
 async function uploadFromActions(sarifPath, gitHubVersion, apiDetails, logger) {
-    return await uploadFiles(getSarifFilePaths(sarifPath), (0, repository_1.parseRepositoryNwo)(util.getRequiredEnvParam("GITHUB_REPOSITORY")), await actionsUtil.getCommitOid(), await actionsUtil.getRef(), await actionsUtil.getAnalysisKey(), actionsUtil.getOptionalInput("category"), util.getRequiredEnvParam("GITHUB_WORKFLOW"), actionsUtil.getWorkflowRunID(), actionsUtil.getRequiredInput("checkout_path"), actionsUtil.getRequiredInput("matrix"), gitHubVersion, apiDetails, logger);
+    return await uploadFiles(getSarifFilePaths(sarifPath), (0, repository_1.parseRepositoryNwo)(util.getRequiredEnvParam("GITHUB_REPOSITORY")), await actionsUtil.getCommitOid(actionsUtil.getRequiredInput("checkout_path")), await actionsUtil.getRef(), await actionsUtil.getAnalysisKey(), actionsUtil.getOptionalInput("category"), util.getRequiredEnvParam("GITHUB_WORKFLOW"), actionsUtil.getWorkflowRunID(), actionsUtil.getRequiredInput("checkout_path"), actionsUtil.getRequiredInput("matrix"), gitHubVersion, apiDetails, logger);
 }
 exports.uploadFromActions = uploadFromActions;
 // Uploads a single sarif file or a directory of sarif files
diff --git a/lib/upload-lib.js.map b/lib/upload-lib.js.map
index e3d18e9bdc..f47be54946 100644
--- a/lib/upload-lib.js.map
+++ b/lib/upload-lib.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/pr-checks/checks/with-checkout-path.yml b/pr-checks/checks/with-checkout-path.yml
new file mode 100644
index 0000000000..369f716cac
--- /dev/null
+++ b/pr-checks/checks/with-checkout-path.yml
@@ -0,0 +1,48 @@
+name: "Use a custom `checkout_path`"
+description: "Checks that a custom `checkout_path` will find the proper commit_oid"
+# Build tracing currently does not support Windows 2022, so use `windows-2019` instead of
+# `windows-latest`.
+# Must test on all three platforms since this test does path manipulation
+os: [ubuntu-latest, macos-latest, windows-2019]
+steps:
+  # Check out the actions repo again, but at a different location.
+  # choose an arbitrary SHA so that we can later test that the commit_oid is not from main
+  - uses: actions/checkout@v2
+    with:
+      ref: 474bbf07f9247ffe1856c6a0f94aeeb10e7afee6
+      path: x/y/z/some-path
+  - uses: ./../action/init
+    with:
+      tools: ${{ steps.prepare-test.outputs.tools-url }}
+      # it's enough to test one compiled language and one interpreted language
+      languages: java,javascript
+      source-path: x/y/z/some-path/tests/multi-language-repo
+      debug: true
+
+  - name: Build code
+    shell: bash
+    run: x/y/z/some-path/tests/multi-language-repo/build.sh
+  - uses: ./../action/analyze
+    with:
+      checkout_path: x/y/z/some-path/tests/multi-language-repo
+      ref: v1.1.0
+      sha: 474bbf07f9247ffe1856c6a0f94aeeb10e7afee6
+      upload: false
+    env:
+      TEST_MODE: true
+  - uses: ./../action/upload-sarif
+    with:
+      ref: v1.1.0
+      sha: 474bbf07f9247ffe1856c6a0f94aeeb10e7afee6
+      checkout_path: x/y/z/some-path/tests/multi-language-repo
+    env:
+      TEST_MODE: true
+
+  - name: Verify SARIF
+    run: |
+      cat ../results/java.sarif
+      echo '------------------------------------'
+      echo '------------------------------------'
+      echo '------------------------------------'
+      echo '------------------------------------'
+      cat ../results/javascript.sarif
diff --git a/src/actions-util.ts b/src/actions-util.ts
index 2776635672..08c656505b 100644
--- a/src/actions-util.ts
+++ b/src/actions-util.ts
@@ -60,7 +60,10 @@ export function getToolCacheDirectory(): string {
 /**
  * Gets the SHA of the commit that is currently checked out.
  */
-export const getCommitOid = async function (ref = "HEAD"): Promise<string> {
+export const getCommitOid = async function (
+  checkoutPath: string,
+  ref = "HEAD"
+): Promise<string> {
   // Try to use git to get the current commit SHA. If that fails then
   // log but otherwise silently fall back to using the SHA from the environment.
   // The only time these two values will differ is during analysis of a PR when
@@ -83,6 +86,7 @@ export const getCommitOid = async function (ref = "HEAD"): Promise<string> {
             process.stderr.write(data);
           },
         },
+        cwd: checkoutPath,
       }
     ).exec();
     return commitOid.trim();
@@ -107,6 +111,7 @@ export const determineMergeBaseCommitOid = async function (): Promise<
   }
 
   const mergeSha = getRequiredEnvParam("GITHUB_SHA");
+  const checkoutPath = getRequiredInput("checkout_path");
 
   try {
     let commitOid = "";
@@ -134,6 +139,7 @@ export const determineMergeBaseCommitOid = async function (): Promise<
             process.stderr.write(data);
           },
         },
+        cwd: checkoutPath,
       }
     ).exec();
 
@@ -498,6 +504,10 @@ export async function getRef(): Promise<string> {
   // or in the form "refs/pull/N/merge" on a pull_request event
   const refInput = getOptionalInput("ref");
   const shaInput = getOptionalInput("sha");
+  const checkoutPath =
+    getOptionalInput("checkout_path") ||
+    getOptionalInput("source-root") ||
+    getRequiredEnvParam("GITHUB_WORKSPACE");
 
   const hasRefInput = !!refInput;
   const hasShaInput = !!shaInput;
@@ -526,7 +536,7 @@ export async function getRef(): Promise<string> {
     return ref;
   }
 
-  const head = await getCommitOid("HEAD");
+  const head = await getCommitOid(checkoutPath, "HEAD");
 
   // in actions/checkout@v2 we can check if git rev-parse HEAD == GITHUB_SHA
   // in actions/checkout@v1 this may not be true as it checks out the repository
@@ -535,8 +545,10 @@ export async function getRef(): Promise<string> {
   // git git-parse GITHUB_REF == git rev-parse HEAD instead.
   const hasChangedRef =
     sha !== head &&
-    (await getCommitOid(ref.replace(/^refs\/pull\//, "refs/remotes/pull/"))) !==
-      head;
+    (await getCommitOid(
+      checkoutPath,
+      ref.replace(/^refs\/pull\//, "refs/remotes/pull/")
+    )) !== head;
 
   if (hasChangedRef) {
     const newRef = ref.replace(pull_ref_regex, "refs/pull/$1/head");
diff --git a/src/upload-lib.ts b/src/upload-lib.ts
index ed01be097d..e370c98562 100644
--- a/src/upload-lib.ts
+++ b/src/upload-lib.ts
@@ -165,7 +165,9 @@ export async function uploadFromActions(
   return await uploadFiles(
     getSarifFilePaths(sarifPath),
     parseRepositoryNwo(util.getRequiredEnvParam("GITHUB_REPOSITORY")),
-    await actionsUtil.getCommitOid(),
+    await actionsUtil.getCommitOid(
+      actionsUtil.getRequiredInput("checkout_path")
+    ),
     await actionsUtil.getRef(),
     await actionsUtil.getAnalysisKey(),
     actionsUtil.getOptionalInput("category"),